SASUF Satellite Events 2024
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SASUF Satellite Events 13-14 May 2024

The Satellite Events are a part of the SASUF Research and Innovation Week 2024, and are organised across Sweden. Some are also hybrid/online. These events are free and open to everyone. To make networking easier, make sure that your profile is public and up to date with a short presentation, picture, and contact details.

The South Africa-Sweden University Forum (SASUF) is strategic internationalisation project with the overall aim of strengthening ties between Sweden and South Africa in research, education and innovation. Read more about SASUF here or on the SASUF website.

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Tuesday, May 14 • 09:00 - 16:00
HYBRID: Elucidating plant-pathogen interactions using genome sequences and open-source tools

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We will broadcast the event with Zoom to enable researchers from all over South Africa and Sweden to participate

Plant disease is a major burden across the world. With the changes in global climate, the spread of pathogens to new ecosystems is becoming an increasing threat to global food security and safety. Researchers are producing high quality genomic and transcriptomic data for various agricultural systems in unseen volumes. The data generated by these methods contains a wealth of information about how plants interact with their environment with regards to biotic and abiotic stresses. The main challenge for researchers is knowing what methods are applicable and available to them to extract the information from the data, and knowing how to interpret the massive volume of results one can obtain from this avenue of research. With this workshop we will showcase how reference genomes from plants and their associated pathogens can be used to elucidate the method of interactions these systems share. We will use sugar beet and its fungal pathogen, Cercospora beticola, as a model system for this workshop as sugar beet is a valuable commodity within both the Swedish and South African economies. The pathogen is yield-limiting for sugar beet crops in South Africa in summer rainfall areas in summer, and is a significant problem in Europe as well. We will use open source and publicly available tools to show how genome annotation can be used to determine the genes involved in plant immunity as well as genes involved in pathogenicity harboured within the fungal genome. We will showcase tools that predict protein structure, as well as sites of interaction within the proteins. We will also show how the domains of interaction are influenced by different evolutionary pressures than regions in the genome that are not involved in the evolutionary arms race between plants and pathogens.
The tools we will showcase will be applicable to all systems for which reference genomes exist, and with this, we hope to engage the SASUF community on a larger scale. The tools and methods we will show can also be used to answer many other questions about genomes and interactions between plants and their environment.

With DLF, our industry-based partner, we will show how the advances in research at universities support the growth of private industry, and how collaborations with industry partners can foster a productive research environment. Ida Lager, the program study coordinator of the M.Sc. program towards plant breeding and protection at SLU, will facilitate a discussion on how researchers of all levels can place themselves in a better position to collaborate with industry partners, as well as preparing themselves for a career in industry.

Our event will consist of two parts, and participants are welcome to join either or both sessions. In the morning, we will showcase the power of using whole genomes by demonstrating the bioinformatic tools used to conduct various type of analyses. This will be followed by showing examples of how to interpret the results. In the afternoon, we will discuss future research questions that can be answered using bioinformatics within the research community. We will also facilitate a discussion with participants that may lead to further collaborations and educational exchanges. Data and scripts used for the workshop will be freely available following the meeting. The data generated together with the scripts will be hosted on repository such as GitHub. The repository will be open to the participants. We will ensure that the content of the meeting will be accessible to students as well as informative to more senior researchers. The primary aim of our workshop will be to launch conversations about using the ever increasing amount of data from both Sweden and South African institutes to further research and education of students. We believe that co-operations between South African and Swedish universities will greatly benefit students from both countries to engage in bioinformatics.

Keywords: Genomics, plant-pathogen interactions, bioinformatics, sugar beet, agriculture

This event is in collaboration with the PlantLink Fascination of Plants day: https://plantday18may.org/


Mark Laing

University of KwaZulu-Natal
avatar for Dr. Lizel Potgieter

Dr. Lizel Potgieter

Bioinformatician, Swedish University of Agricultural Sciences
I am a member of the SLU Bioinformatics Infrastructure (SLUBI) team. We serve the SLU community by helping researchers to plan experiments, analyse the bioinformatics data, and prepare papers for publication. We are also involved in teaching various bioinformatics courses at SLU.You... Read More →

Tuesday May 14, 2024 09:00 - 16:00 CEST
SLU Campus, Alnarp
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